9C1H | pdb_00009c1h

Rhesus rotavirus (upright structure at 2.88 Angstrom resolution)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Rotavirus structure

Jenni, S.Herrmann, T.De Sautu, M.Harrison, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid glycoprotein VP7326Simian rotavirus A strain RRVMutation(s): 0 
UniProt
Find proteins for P12476 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Explore P12476 
Go to UniProtKB:  P12476
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12476
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP4C [auth 2],
D [auth 3],
E [auth 4]
776Simian rotavirus A strain RRVMutation(s): 0 
UniProt
Find proteins for P12473 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Explore P12473 
Go to UniProtKB:  P12473
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12473
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Inner capsid protein VP2F [auth A],
G [auth B]
887Simian rotavirus A strain RRVMutation(s): 0 
UniProt
Find proteins for B3F2X3 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Explore B3F2X3 
Go to UniProtKB:  B3F2X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3F2X3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Intermediate capsid protein VP6397Simian rotavirus A strain RRVMutation(s): 0 
UniProt
Find proteins for B2BN53 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Explore B2BN53 
Go to UniProtKB:  B2BN53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2BN53
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseRA [auth a]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CD [auth V]
EC [auth Q]
EF [auth x]
JF [auth y]
KE [auth t]
CD [auth V],
EC [auth Q],
EF [auth x],
JF [auth y],
KE [auth t],
LD [auth X],
NC [auth S],
PE [auth u],
QD [auth Y],
SA [auth 0],
SC [auth T],
UE [auth v],
VD [auth Z],
XA [auth 1],
XC [auth U],
ZB [auth P],
ZE [auth w]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AE [auth f]
BE [auth f]
CB [auth C]
CE [auth g]
EB [auth C]
AE [auth f],
BE [auth f],
CB [auth C],
CE [auth g],
EB [auth C],
EE [auth h],
FB [auth D],
FE [auth i],
GB [auth E],
GE [auth i],
HB [auth F],
IE [auth j],
JB [auth F],
JE [auth k],
KB [auth G],
LB [auth H],
MB [auth I],
NB [auth I],
PB [auth J],
QB [auth K],
RB [auth L],
SB [auth L],
UB [auth M],
VB [auth N],
WB [auth O],
YB [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth 1]
AC [auth P]
AD [auth U]
AF [auth w]
BB [auth 1]
AB [auth 1],
AC [auth P],
AD [auth U],
AF [auth w],
BB [auth 1],
BC [auth P],
BD [auth U],
BF [auth w],
CC [auth P],
CF [auth w],
DC [auth P],
DD [auth V],
DF [auth w],
ED [auth V],
FC [auth Q],
FD [auth V],
FF [auth x],
GC [auth Q],
GD [auth V],
GF [auth x],
HC [auth Q],
HD [auth W],
HF [auth x],
IC [auth Q],
ID [auth W],
IF [auth x],
JC [auth R],
JD [auth W],
KC [auth R],
KD [auth W],
KF [auth y],
LC [auth R],
LE [auth t],
LF [auth y],
MC [auth R],
MD [auth X],
ME [auth t],
MF [auth y],
ND [auth X],
NE [auth t],
NF [auth y],
OC [auth S],
OD [auth X],
OE [auth t],
PC [auth S],
PD [auth X],
QC [auth S],
QE [auth u],
RC [auth S],
RD [auth Y],
RE [auth u],
SD [auth Y],
SE [auth u],
TA [auth 0],
TC [auth T],
TD [auth Y],
TE [auth u],
UA [auth 0],
UC [auth T],
UD [auth Y],
VA [auth 0],
VC [auth T],
VE [auth v],
WA [auth 0],
WC [auth T],
WD [auth Z],
WE [auth v],
XD [auth Z],
XE [auth v],
YA [auth 1],
YC [auth U],
YD [auth Z],
YE [auth v],
ZA [auth 1],
ZC [auth U],
ZD [auth Z]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
DB [auth C]
DE [auth h]
HE [auth j]
IB [auth F]
OB [auth J]
DB [auth C],
DE [auth h],
HE [auth j],
IB [auth F],
OB [auth J],
TB [auth M],
XB [auth O]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
FA [auth f]
GA [auth g]
H [auth C]
HA [auth h]
I [auth D]
FA [auth f],
GA [auth g],
H [auth C],
HA [auth h],
I [auth D],
IA [auth i],
J [auth E],
JA [auth j],
K [auth F],
KA [auth k],
L [auth G],
M [auth H],
N [auth I],
O [auth J],
P [auth K],
Q [auth L],
R [auth M],
S [auth N],
T [auth O]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5127

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA13202

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release